Mendelian Randomization Analysis: Smoking Status and Alzheimer's Disease

By Dr. Shea Andrews, generated on 2018-09-06


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Data sources

***[Smoking Status*** (Canela-Xandri et al BioRxiv 2018)]: Summary statisitcs for Smoking Status were genereated from the UK Biobank with participatns asked weather they were never, former or current somkers. Results were reported in GeneATLAS, a large database of associations between hundreds of traits and millions of variants using the UK Biobank cohort.

Late Onset Alzheimer’s disease Lambert et al 2013: The International Genomics of Alzheimer’s Project (IGAP) is a meta-analysis of 4 previously published GWAS datasets: the European Alzheimer’s Disease Imitative (EADI), the Alzheimer Disease Genetics Consortium (ADGC), Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE), and Genetic and Environmental Risk in AD (GERAD) and includes a sample of 17,008 LOAD cases and 37,154 cognitively normal elder controls. Participants in IGAP were of European ancestry, the average age was 71 and 58.4% of participants were women.

Alzheimer’s Age of Onset Surivial Huang et al 2017: A GWAS of age of onset in LOAD was conducted in 14,406 AD case samples and 25,849 control samples from the IGAP using Cox proportional hazard regressions. Participants were of European ancestry, in cases the the average AAO was 74.8 and 61.7% were women, in controls the average AAE was 79.0 and 59.6% were women.

CSF Ab42, tau & ptau Deming et al 2017: A GWAS of CSF AB42, ptau and tau levels (pg/mL) was conducted in 3,146 participants. Participants were of Eurpean ancestry.

Hippocampal Volume Hibar et al 2017: A GWAS of hippocampal volume perfomed in 26,814 (ENIGMA and CHARGE consortiums) individules of European Ancestry discovered 9 independent loci.

Instrumental Variables

LD Clumping: For standard two sample MR it is important to ensure that the instruments for the exposure are independent. LD clumping can be performed using the data_clump function from the TwoSampleMR package, which uses EUR samples from the 1000 genomes project to estimate LD between SNPs and amonst SNPs that have and LD above a given threshold, only the SNP with the lowest p-value will be retained.

Proxy SNPs: SNPs associated with Smoking Status were extracted from the GWAS of LOAD, AAOS, AB42, ptau and tau. Where SNPs were not available in the outcome GWAS, the EUR thousand genomes was queried to identified potential proxy SNPs that are in linkage disequilibrium (r2 > 0.8) of the missing SNP.

Smoking Status

Smoking Status: 9411 SNPs (Table 1) were assoicated with were associated with Smoking Status at p < 5e-8. After LD clumping, 9189 of 9411 SNPs were removed.

Table 1: Independent SNPS associated with Smoking Status


LOAD

Of the the 222 SNPs associated with Smoking Status, 206 were available in the LOAD GWAS (Table 2).

Table 2: SNPS associated with Smoking Status avalible in LOAD GWAS


AAOS

Of the the 222 SNPs associated with Smoking Status, 221 were available in the AAOS GWAS (Table 3).

Table 3: SNPS associated with available in AAOS GWAS


AB42

Of the the 222 SNPs associated with Smoking Status, 175 were available in the CSF AB42 GWAS (Table 4).

Table 4: SNPS associated with Smoking Status avalible in ab42 GWAS


Ptau

Of the the 222 SNPs associated with Smoking Status, 191 were available in the CSF Ptau GWAS (Table 5).

Table 5: SNPS associated with Smoking Status avalible in Ptau GWAS


Tau

Of the the 222 SNPs associated with Smoking Status, 175 were available in the CSF Tau GWAS (Table 6).

Table 6: SNPS associated with Smoking Status avalible in tau GWAS


Hippocampal volume

Of the the 222 SNPs associated with Smoking Status, 215 were available in the Hippocampal volume (Table 7).

Table 7: SNPS associated with Smoking Status avalible in Hippocampal volume GWAS


Data harmonization

Harmonize the exposure and outcome datasets so that the effect of a SNP on the exposure and the effect of that SNP on the outcome correspond to the same allele. The harmonise_data function from the TwoSampleMR package can be used to perform the harmonization step, by default it try’s to infer the forward strand alleles using allele frequency information. EAF were not availbe in the IGAP summary statisitics, as such the allele frequencies reported in the AAOS anaylsis were used.

Smoking Status ~ LOAD

Table 8: Harmonized Smoking Status and LOAD datasets


Smoking Status ~ AAOS

Table 9: Harmonized Smoking Status and AAOS datasets


Smoking Status ~ AB42

Table 10: Harmonized Smoking Status and AB42 datasets


Smoking Status ~ Ptau

Table 11: Harmonized Smoking Status and Ptau datasets


Smoking Status ~ Tau

Table 12: Harmonized Smoking Status and Tau datasets


Smoking Status ~ Hippocampal Volume

Table 13: Harmonized Smoking Status and Hippocampal Volume datasets



Pleiotropy

Pleiotropy was assesed using Mendelian Randomization Pleiotropy RESidual Sum and Outlier (MR-PRESSO), that allows for the evlation of evaluation of horizontal pleiotropy in a standared MR model. MR-PRESSO performs a global test for detection of horizontal pleiotropy and correction of pleiotropy via outlier removal.

Smoking Status ~ LOAD: The MR-PRESSO global test for pleiotropy was significant (p = 0.0105). The following SNPs were removed due to pleiotropy: No significant outliers

Smoking Status ~ AAOS: The MR-PRESSO global test for pleiotropy was non-significant.

Smoking Status ~ AB42: The MR-PRESSO global test for pleiotropy was non-significant.

Smoking Status ~ Ptau: The MR-PRESSO global test for pleiotropy was non-significant.

Smoking Status ~ Tau: The MR-PRESSO global test for pleiotropy was non-significant..

Smoking Status ~ hippocampal volume: The MR-PRESSO global test for pleiotropy was significant (p = 0.0289). The following SNPs were removed due to pleiotropy: rs11693702

Mendelian Randomization Analysis

To obtain an overall estimate of causal effect, the SNP-exposure (Major Depressive Disorder) and SNP-outcome coefficients (Alzheimer’s disease and Alzheimer’s Age of Onset) were combined in 1) a random-effects meta-analysis using an inverse-variance weighted approach (IVW); 2) a Weighted Median approach; 3) and Egger Regression. IVW is equivalent to a weighted regression of the SNP-outcome coefficients on the SNP-exposure coefficients with the intercept constrained to zero. This method assumes that all variants are valid instrumental variables based on the Mendelian randomization assumptions. The causal estimate of the IVW analysis expresses the causal increase in the outcome (or log odds of the outcome for a binary outcome) per unit change in the exposure. Weighted median MR allows for 50% of the instrumental variables to be invalid. MR-Egger regression allows all the instrumental variables to be subject to direct effects (i.e. horizontal pleiotropy), with the intercept representing bias in the causal estimate due to pleiotropy and the slope representing the causal estimate.

Smoking Status ~ LOAD


Figure 1 illustrates the SNP-specific associations with Smoking Status versus the association between each SNP and risk of LOAD.

Fig. 1: Scatterplot of SNP effects for the association of Trait and LOAD

Fig. 1: Scatterplot of SNP effects for the association of Trait and LOAD


Figure 2 and Table 1 shows the SNP-specific effects and overall IVW, weighted median and Egger regression causal estimates of genetically predicted Smoking Status on risk of LOAD.

Fig. 2: Forrest plot of Wald ratios and 95% CIs for SNP-specific and overall IVW, Weighted median and Egger associations

Fig. 2: Forrest plot of Wald ratios and 95% CIs for SNP-specific and overall IVW, Weighted median and Egger associations


Table 1: MR estimates for Smoking Status and LOAD


Figure 3 shows a funnel plot to detect pleiotropy and Table 2 show the results of Cochrans Q heterogeneity test to assess for the presence of pleiotropy.

Fig. 3: Funnel plot of the Trait – LOAD causal estimates against their precession

Fig. 3: Funnel plot of the Trait – LOAD causal estimates against their precession


Table 2: Heterogenity tests for Smoking Status and LOAD
Table 3: Test for directional pleitropy for Smoking Status and LOAD

Smoking Status ~ AAOS


Figure 4 illustrates the SNP-specific associations with Smoking Status versus the association between each SNP and AAOS.

Fig. 4: Scatterplot of SNP effects for the association of Trait and AAOS

Fig. 4: Scatterplot of SNP effects for the association of Trait and AAOS


Figure 5 and Table 4 shows the SNP-specific effects and overall IVW, weighted median and Egger regression causal estimates of genetically predicted Smoking Status on AAOS.

Fig. 5: Forrest plot of Wald ratios and 95% CIs for SNP-specific and overall IVW, Weighted median and Egger associations

Fig. 5: Forrest plot of Wald ratios and 95% CIs for SNP-specific and overall IVW, Weighted median and Egger associations


Table 4: MR estimates for Smoking Status and AAOS


Figure 6 shows a funnel plot to detect pleiotropy and Table 5 show the results of Cochrans Q heterogeneity test to assess for the presence of pleiotropy.

Fig. 6:  Funnel plot of the traitohol Conumption – AAOS causal estimates against their precession

Fig. 6: Funnel plot of the traitohol Conumption – AAOS causal estimates against their precession


Table 5: Heterogenity tests for Smoking Status and AAOS
Table 6: Test for directional pleitropy for Smoking Status and AAOS

Smoking Status ~ AB42


Figure 1 illustrates the SNP-specific associations with Smoking Status versus the association between each SNP and AB42.

Fig. 1: Scatterplot of SNP effects for the association of trait and AB42

Fig. 1: Scatterplot of SNP effects for the association of trait and AB42


Figure 2 and Table 7 shows the SNP-specific effects and overall IVW, weighted median and Egger regression causal estimates of genetically predicted Smoking Status CSF AB42 levels.

Fig. 2: Forrest plot of Wald ratios and 95% CIs for SNP-specific and overall IVW, Weighted median and Egger associations

Fig. 2: Forrest plot of Wald ratios and 95% CIs for SNP-specific and overall IVW, Weighted median and Egger associations


Table 7: MR estimates for Smoking Status and AB42


Figure 3 shows a funnel plot to detect pleiotropy and Table 8 show the results of Cochrans Q heterogeneity test to assess for the presence of pleiotropy.

Fig. 3: Funnel plot of the trait – AB42 causal estimates against their precession

Fig. 3: Funnel plot of the trait – AB42 causal estimates against their precession


Table 8: Heterogenity tests for Smoking Status and AB42
Table 9: Test for directional pleitropy for Smoking Status and AB42

Smoking Status ~ Ptau


Figure 1 illustrates the SNP-specific associations with Smoking Status versus the association between each SNP and risk of Ptau.

Fig. 1: Scatterplot of SNP effects for the association of trait and Ptau

Fig. 1: Scatterplot of SNP effects for the association of trait and Ptau


Figure 2 and Table 9 shows the SNP-specific effects and overall IVW, weighted median and Egger regression causal estimates of genetically predicted Smoking Status on risk of Ptau.

Fig. 2: Forrest plot of Wald ratios and 95% CIs for SNP-specific and overall IVW, Weighted median and Egger associations

Fig. 2: Forrest plot of Wald ratios and 95% CIs for SNP-specific and overall IVW, Weighted median and Egger associations


Table 9: MR estimates for Smoking Status and Ptau


Figure 3 shows a funnel plot to detect pleiotropy and Table 10 show the results of Cochrans Q heterogeneity test to assess for the presence of pleiotropy.

Fig. 3: Funnel plot of the trait – Ptau causal estimates against their precession

Fig. 3: Funnel plot of the trait – Ptau causal estimates against their precession


Table 10: Heterogenity tests for Smoking Status and Ptau
Table 11: Test for directional pleitropy for Smoking Status and Ptau

Smoking Status ~ Tau


Figure 1 illustrates the SNP-specific associations with Smoking Status versus the association between each SNP and CSF Tau levels.

Fig. 1: Scatterplot of SNP effects for the association of trait and Tau

Fig. 1: Scatterplot of SNP effects for the association of trait and Tau


Figure 2 and Table 12 shows the SNP-specific effects and overall IVW, weighted median and Egger regression causal estimates of genetically predicted Smoking Status on risk of Tau.

Fig. 2: Forrest plot of Wald ratios and 95% CIs for SNP-specific and overall IVW, Weighted median and Egger associations

Fig. 2: Forrest plot of Wald ratios and 95% CIs for SNP-specific and overall IVW, Weighted median and Egger associations


Table 12: MR estimates for Smoking Status and Tau


Figure 3 shows a funnel plot to detect pleiotropy and Table 13 show the results of Cochrans Q heterogeneity test to assess for the presence of pleiotropy.

Fig. 3: Funnel plot of the trait – Tau causal estimates against their precession

Fig. 3: Funnel plot of the trait – Tau causal estimates against their precession


Table 14: Heterogenity tests for Smoking Status and Tau
Table 15: Test for directional pleitropy for Smoking Status and Tau

Smoking Status ~ HV


Figure 1 illustrates the SNP-specific associations with Smoking Status versus the association between each SNP and hippocampal volume.

Fig. 1: Scatterplot of SNP effects for the association of trait and hippocampal volume

Fig. 1: Scatterplot of SNP effects for the association of trait and hippocampal volume


Figure 2 and Table 12 shows the SNP-specific effects and overall IVW, weighted median and Egger regression causal estimates of genetically predicted Smoking Status on risk of hippocampal volume.

Fig. 2: Forrest plot of Wald ratios and 95% CIs for SNP-specific and overall IVW, Weighted median and Egger associations

Fig. 2: Forrest plot of Wald ratios and 95% CIs for SNP-specific and overall IVW, Weighted median and Egger associations


Table 12: MR estimates for Smoking Status and hippocampal volume


Figure 3 shows a funnel plot to detect pleiotropy and Table 13 show the results of Cochrans Q heterogeneity test to assess for the presence of pleiotropy.

Fig. 3: Funnel plot of the trait – hippocampal volume causal estimates against their precession

Fig. 3: Funnel plot of the trait – hippocampal volume causal estimates against their precession


Table 14: Heterogenity tests for Smoking Status and hippocampal volume
Table 15: Test for directional pleitropy for Smoking Status and hippocampal volume


MR analysis results